Small RNA data description

Introduction

This page is intended to provide an overview of the current state of small RNA sequencing in the FANTOM5 project. It addresses the raw material and methods used in sequencing small RNA, methods used to map the sequences, data normalization strategies, and some quality control measures. For discussion on the F5 small RNA paper, please see this [ page]. For an overview of all noncoding RNA data and resources in FANTOM5, see this [ page].

Sequencing Methods

Small RNA for the FANTOM5 project was sequenced using the Illumina TruSeq kit, with 24 distinct samples multiplexed in a single Illumina HiSeq2000 lane. In each lane, a control (the standard mouse whole body, embryo E17.5 internal control used for all of FANTOM5) was sequenced with the same barcode.

Source RNA

To this point, small RNA sequencing has focused on the FANTOM5 panel of primary cells. Primary cell RNA was selected for small RNA-seq based on the following conditions: 1) availability of the sequences at the time the sequencing order was made and 2) preparation of the original RNA sample before delivery to RIKEN OSC did not exclude small RNAs.

The list of all samples sequenced is attached [ here].